public class PTM extends ExperimentObject
Modifier and Type | Field and Description |
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static int |
MODAA
Modification at particular amino acids.
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static int |
MODC
Modification at the C terminus of a protein.
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static int |
MODCAA
Modification at the C terminus of a protein at particular amino acids.
|
static int |
MODCP
Modification at the C terminus of a peptide.
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static int |
MODCPAA
Modification at the C terminus of a peptide at particular amino acids.
|
static int |
MODMAX
The max number of modification types.
|
static int |
MODN
Modification at the N terminus of a protein.
|
static int |
MODNAA
Modification at the N terminus of a protein at particular amino acids.
|
static int |
MODNP
Modification at the N terminus of a peptide.
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static int |
MODNPAA
Modification at the N terminus of a peptide at particular amino acids.
|
Constructor and Description |
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PTM()
Constructor for the modification.
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PTM(int type,
String name,
Double mass,
ArrayList<String> residues)
Simple constructor for a PTM.
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PTM(int type,
String name,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern)
Constructor for a reference modification.
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PTM(int type,
String name,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern,
CvTerm cvTerm)
Constructor for a reference modification.
|
Modifier and Type | Method and Description |
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void |
addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss.
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void |
addReporterIon(ReporterIon reporterIon)
Adds a reporter ion.
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AtomChain |
getAtomChainAdded()
Returns the atom chain added.
|
AtomChain |
getAtomChainRemoved()
Returns the atom chain removed.
|
CvTerm |
getCvTerm()
Returns the CV term associated with this PTM.
|
String |
getHtmlTooltip()
Returns information about the PTM as an HTML tooltip.
|
double |
getMass()
Getter for the mass difference induced by this modification.
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String |
getName()
Getter for the modification name.
|
ArrayList<NeutralLoss> |
getNeutralLosses()
Returns the neutral losses possibly encountered with this modification.
|
AminoAcidPattern |
getPattern()
Returns the amino acid pattern targeted by this modification.
|
ArrayList<ReporterIon> |
getReporterIons()
Returns the reporter ions possibly encountered with this modification.
|
double |
getRoundedMass()
Getter for the rounded mass difference induced by this modification.
|
double |
getRoundedMass(int numberOfDecimals)
Getter for the rounded mass difference induced by this modification.
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String |
getShortName()
Getter for the short modification name.
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int |
getType()
Getter for the modification type.
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boolean |
isCTerm()
Returns true if the PTM is a c-term PTM.
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boolean |
isNTerm()
Returns true if the PTM is an n-term PTM.
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boolean |
isSameAs(PTM anotherPTM)
Returns true if the PTM is the same as another one.
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boolean |
isSameAtomicComposition(PTM anotherPTM)
Returns true if the atomic composition of the PTM is the same as another
one.
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boolean |
isSamePattern(PTM anotherPTM)
Returns true if the targeted pattern of the PTM is the same as another
one.
|
boolean |
isStandardSearch()
Indicates whether a modification can be searched with standard search
engines, i.e., true if it targets a single amino acid position, false if
it targets a complex pattern.
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void |
setAtomChainAdded(AtomChain atomChainAdded)
Sets the atom chain added.
|
void |
setAtomChainRemoved(AtomChain atomChainRemoved)
Sets the atom chain removed.
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void |
setCvTerm(CvTerm cvTerm)
Set the CV term associated with this PTM.
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void |
setName(String name)
Sets the PTM name.
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void |
setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)
Sets the neutral losses possibly encountered with this modification.
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void |
setPattern(AminoAcidPattern pattern)
Sets the amino acid pattern targeted by this modification.
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void |
setReporterIons(ArrayList<ReporterIon> reporterIons)
Sets the reporter ions possibly encountered with this modification.
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void |
setShortName(String shortName)
Sets the short PTM name.
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addUrParam, getParameterKey, getUrParam
public static final int MODAA
public static final int MODN
public static final int MODNAA
public static final int MODC
public static final int MODCAA
public static final int MODNP
public static final int MODNPAA
public static final int MODCP
public static final int MODCPAA
public static final int MODMAX
public PTM()
public PTM(int type, String name, String shortName, AtomChain atomChainAdded, AtomChain atomChainRemoved, AminoAcidPattern aminoAcidPattern)
type
- type of modification according to static attributesname
- name of the modificationshortName
- short name of the modificationatomChainAdded
- atomic composition of the molecule addedatomChainRemoved
- atomic composition of the molecule removedaminoAcidPattern
- residue pattern affected by this modificationpublic PTM(int type, String name, String shortName, AtomChain atomChainAdded, AtomChain atomChainRemoved, AminoAcidPattern aminoAcidPattern, CvTerm cvTerm)
type
- type of modification according to static attributesname
- name of the modificationshortName
- short name of the modificationatomChainAdded
- atomic composition of the molecule addedatomChainRemoved
- atomic composition of the molecule removedaminoAcidPattern
- residue pattern affected by this modificationcvTerm
- the CV term associated with this PTM, null if not setpublic PTM(int type, String name, Double mass, ArrayList<String> residues)
type
- type of modification according to static attributesname
- name of the modificationmass
- the mass of the modificationresidues
- list of residues possibly targeted by this modificationpublic int getType()
public String getName()
public void setName(String name)
name
- the PTM namepublic String getShortName()
public void setShortName(String shortName)
shortName
- the PTM namepublic double getMass()
public double getRoundedMass(int numberOfDecimals)
numberOfDecimals
- the number of decimals to round topublic double getRoundedMass()
public AtomChain getAtomChainAdded()
public void setAtomChainAdded(AtomChain atomChainAdded)
atomChainAdded
- the atom chain addedpublic AtomChain getAtomChainRemoved()
public void setAtomChainRemoved(AtomChain atomChainRemoved)
atomChainRemoved
- the atom chain removedpublic boolean isSameAtomicComposition(PTM anotherPTM)
anotherPTM
- the PTM to compare topublic boolean isSamePattern(PTM anotherPTM)
anotherPTM
- the PTM to compare topublic boolean isSameAs(PTM anotherPTM)
anotherPTM
- another PTMpublic ArrayList<NeutralLoss> getNeutralLosses()
public void setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)
neutralLosses
- the neutral losses possibly encountered with this
modificationpublic void addNeutralLoss(NeutralLoss neutralLoss)
neutralLoss
- the new neutral losspublic ArrayList<ReporterIon> getReporterIons()
public void setReporterIons(ArrayList<ReporterIon> reporterIons)
reporterIons
- the reporter ions possibly encountered with this
modificationpublic void addReporterIon(ReporterIon reporterIon)
reporterIon
- the reporter ion to addpublic AminoAcidPattern getPattern()
public void setPattern(AminoAcidPattern pattern)
pattern
- the amino acid pattern targeted by this modificationpublic boolean isStandardSearch()
public boolean isNTerm()
public boolean isCTerm()
public String getHtmlTooltip()
public CvTerm getCvTerm()
public void setCvTerm(CvTerm cvTerm)
cvTerm
- the cvTerm to setCopyright © 2016. All rights reserved.